#!/usr/bin/env python3

import argparse

k=64

parser = argparse.ArgumentParser(description="Analyse diffusion maps.

The following plots will be made:

* a plot of the eigenvalues, useful for making an educated guess on the
  dimensionality (see REFERENCE)
* 3D

", formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('diffusion-map', help='file containing the diffusion map')
parser.add_argument('output', help='Directory to save plots in')
parser.add_argument('-k', metavar='k', type=int, help='number of neirest neighbours to use', default=64)
parser.add_argument('--points', type=int, help='number of sampled points to use', default=2048)
parser.add_argument('--eigenvectors', type=int, help='only calculate this number of eigenvectors', required=False)
parser.add_argument('--normalize', type=bool, help='normalize data before constructing diffusion maps', default=True)
parser.add_argument('--space-clip-percentage', type=int, help='percentage to ignore in each space dimension (for eliminating border effects)', default=25)
parser.add_argument('--start-time', type=int, help='time to start at (percentage-wise)', default=10)
parser.add_argument('--end-time', type=int, help='time to end at (percentage-wise)', default=100)
parser.add_argument('--batch', action=argparse.BooleanOptionalAction, help="Only save plots, don't show them in a GUI")

args = parser.parse_args()

print(args)
